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Alexander J. Ruthenburg

TitleAssociate Professor
InstitutionUniversity of Chicago
DepartmentMolecular Genetics and Cell Biology
AddressChicago IL 60637
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    Collapse Overview 
    Collapse overview
    The unifying theme of my lab is the elucidation of molecular mechanisms underlying management chromatin, the physiological form of the genome. In particular, we are interested in how post translational modifications to histones, newly appreciated DNA modifications and noncoding RNA can control chromatin structure. Our research spans several traditional disciplines, ranging from discovery biochemistry and genome-scale measurements to mechanistic characterization with biophysical methods coupled with X-Ray structure to address fundamental questions in chromatin biology. We have pioneered new technologies to make quantitative local measurements of chromatin components. Projects ideally will transition from discovery biology to detailed molecular and structural investigation.
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    Collapse Biography 
    Collapse education and training
    Rockefeller University , New York, NYPostdoctoral Fellow8/2010Chromatin biochemsitry and epigenetics
    Harvard University , Cambridge, MAPh.D.9/2005Chemical and Structural biology
    Carleton College, Northfield, MNB.A.6/1999Chemistry
    Collapse awards and honors
    2011Kavli Fellow, National Academy of Sciences
    2013 - 2017New Scholar in Aging, Ellison Medical Foundation
    2010 - 2015Neubauer Family Foundation Assistant Professor, University of Chicago
    2010 - 2012 Junior Investigator, Chicago Biomedical Consortium
    2007 - 2010 Irvington Institute Research Fellowship, Cancer Research Institute
    2000 - 2004National Science Foundation Graduate Research Fellow , Harvard University

    Collapse Research 
    Collapse research activities and funding
    17CSA33610126     (Moskowitz & Ruthenburg)Jul 1, 2017
    American Heart Association
    Enhancer transcription as marker and modulator of cardiac regulatory networks
    Role Description: Collaborative Sciences Award
    Role: Co-PI

    RSG-16-248-01-DMC     (Ruthenburg)Jan 1, 2017 - Dec 31, 2020
    American Cancer Society
    Biochemical discovery of new epigenetic pathways linked to leukemia
    Role: Principal Invesitgator

    R01GM115945     (RUTHENBURG, ALEXANDER JACKSON)Apr 6, 2016 - Mar 31, 2021
    Quantitatively probing intra-nucleosomal chromatin variation and function
    Role: Principal Investigator

    R44-HG008907     (Zu-Wen Sun)Dec 15, 2015 - Nov 30, 2017
    Internally calibrated chromatin immunoprecipitation using barcoded nucleosomes
    Role Description: This is a phase II SBIR centered on commercializing the ICeChIP technology developed in my lab. Two products are now on the market, offered by Epicypher, Inc: SNAP-ChIP and CAP-ChIP.
    Role: Co-investigator

    R21HG007426     (RUTHENBURG, ALEXANDER JACKSON)Aug 22, 2013 - May 31, 2015
    Calibrated ChIP-seq: determining local histone modification density genome-wide
    Role: Principal Investigator

    AG-NS-1118-13     (Ruthenburg)Aug 1, 2013 - Aug 1, 2017
    Ellison Medical Foundation
    Discovery of New Epigenetic Pathways involved in stem sell maintenance
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
    Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Kainth AS, Haddad GA, Hall JM, Ruthenburg AJ. Merging short and stranded long reads improves transcript assembly. PLoS Comput Biol. 2023 Oct; 19(10):e1011576. PMID: 37883581; PMCID: PMC10629667.
      Citations:    Fields:    Translation:Cells
    2. Chi P, Lewis PW, Lu C, Lu J, Ruthenburg AJ, Sabari BR, Shechter D, Wan L, Wang GG. Charles David Allis (1951-2023). Nat Genet. 2023 Apr; 55(4):522-523. PMID: 36849658.
      Citations:    Fields:    
    3. Shah RN, Ruthenburg AJ. Specificity Guides Interpretation: On H3K4 Methylation at Enhancers and Broad Promoters. bioRxiv. 2023 Jan 17. PMID: 36711866; PMCID: PMC9882130.
    4. Zeng Y, Fair BJ, Zeng H, Krishnamohan A, Hou Y, Hall JM, Ruthenburg AJ, Li YI, Staley JP. Profiling lariat intermediates reveals genetic determinants of early and late co-transcriptional splicing. Mol Cell. 2022 12 15; 82(24):4681-4699.e8. PMID: 36435176; PMCID: PMC10448999.
      Citations: 6     Fields:    Translation:HumansCells
    5. Richter WF, Shah RN, Ruthenburg AJ. Non-canonical H3K79me2-dependent pathways promote the survival of MLL-rearranged leukemia. Elife. 2021 07 15; 10. PMID: 34263728; PMCID: PMC8315800.
      Citations: 9     Fields:    Translation:HumansCells
    6. Shah RN, Ruthenburg AJ. Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads. PLoS Comput Biol. 2021 04; 17(4):e1008926. PMID: 33872311; PMCID: PMC8084338.
      Citations: 3     Fields:    Translation:HumansCells
    7. Oikawa M, Simeone A, Hormanseder E, Teperek M, Gaggioli V, O'Doherty A, Falk E, Sporniak M, D'Santos C, Franklin VNR, Kishore K, Bradshaw CR, Keane D, Freour T, David L, Grzybowski AT, Ruthenburg AJ, Gurdon J, Jullien J. Epigenetic homogeneity in histone methylation underlies sperm programming for embryonic transcription. Nat Commun. 2020 07 13; 11(1):3491. PMID: 32661239; PMCID: PMC7359334.
      Citations: 10     Fields:    Translation:AnimalsCells
    8. Sun X, Wang Z, Hall JM, Perez-Cervantes C, Ruthenburg AJ, Moskowitz IP, Gribskov M, Yang XH. Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq. PLoS Comput Biol. 2020 02; 16(2):e1007119. PMID: 32040509; PMCID: PMC7034927.
      Citations: 3     Fields:    Translation:HumansAnimalsCells
    9. Grzybowski AT, Shah RN, Richter WF, Ruthenburg AJ. Native internally calibrated chromatin immunoprecipitation for quantitative studies of histone post-translational modifications. Nat Protoc. 2019 12; 14(12):3275-3302. PMID: 31723301; PMCID: PMC7158589.
      Citations: 8     Fields:    Translation:HumansAnimalsCells
    10. Bennett RL, Bele A, Small EC, Will CM, Nabet B, Oyer JA, Huang X, Ghosh RP, Grzybowski AT, Yu T, Zhang Q, Riva A, Lele TP, Schatz GC, Kelleher NL, Ruthenburg AJ, Liphardt J, Licht JD. A Mutation in Histone H2B Represents a New Class of Oncogenic Driver. Cancer Discov. 2019 10; 9(10):1438-1451. PMID: 31337617; PMCID: PMC6774836.
      Citations: 34     Fields:    Translation:HumansAnimalsCells
    11. Shah RN, Grzybowski AT, Cornett EM, Johnstone AL, Dickson BM, Boone BA, Cheek MA, Cowles MW, Maryanski D, Meiners MJ, Tiedemann RL, Vaughan RM, Arora N, Sun ZW, Rothbart SB, Keogh MC, Ruthenburg AJ. Examining the Roles of H3K4 Methylation States with Systematically Characterized Antibodies. Mol Cell. 2018 10 04; 72(1):162-177.e7. PMID: 30244833; PMCID: PMC6173622.
      Citations: 46     Fields:    Translation:HumansCells
    12. Karki S, Kennedy DE, Mclean K, Grzybowski AT, Maienschein-Cline M, Banerjee S, Xu H, Davis E, Mandal M, Labno C, Powers SE, Le Beau MM, Dinner AR, Singh H, Ruthenburg AJ, Clark MR. Regulated Capture of V? Gene Topologically Associating Domains by Transcription Factories. Cell Rep. 2018 08 28; 24(9):2443-2456. PMID: 30157436; PMCID: PMC6310487.
      Citations: 12     Fields:    Translation:HumansAnimalsCells
    13. Maganti HB, Jrade H, Cafariello C, Manias Rothberg JL, Porter CJ, Battaion HL, Khan ST, Howard JP, Li Y, Grzybowski AT, Sabri E, Ruthenburg AJ, Dilworth FJ, Perkins TJ, Sabloff M, Ito CY, Stanford WL, Yockell-Lelièvre J. Targeting the MTF2-MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy. Cancer Discov. 2018 11; 8(11):1376-1389. PMID: 30115703; PMCID: PMC7200079.
      Citations: 23     Fields:    Translation:HumansAnimalsCells
    14. Gupta A, Xu J, Lee S, Tsai ST, Zhou B, Kurosawa K, Werner MS, Koide A, Ruthenburg AJ, Dou Y, Koide S. Facile target validation in an animal model with intracellularly expressed monobodies. Nat Chem Biol. 2018 09; 14(9):895-900. PMID: 30013062; PMCID: PMC6103845.
      Citations: 17     Fields:    Translation:AnimalsCells
    15. Yang XH, Nadadur RD, Hilvering CR, Bianchi V, Werner M, Mazurek SR, Gadek M, Shen KM, Goldman JA, Tyan L, Bekeny J, Hall JM, Lee N, Perez-Cervantes C, Burnicka-Turek O, Poss KD, Weber CR, de Laat W, Ruthenburg AJ, Moskowitz IP. Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm. Elife. 2017 12 27; 6. PMID: 29280435; PMCID: PMC5745077.
      Citations: 26     Fields:    Translation:AnimalsCells
    16. Chen Z, Notti RQ, Ueberheide B, Ruthenburg AJ. Quantitative and Structural Assessment of Histone Methyllysine Analogue Engagement by Cognate Binding Proteins Reveals Affinity Decrements Relative to Those of Native Counterparts. Biochemistry. 2018 01 23; 57(3):300-304. PMID: 29111671; PMCID: PMC5780203.
      Citations: 9     Fields:    Translation:HumansCells
    17. Werner MS, Sullivan MA, Shah RN, Nadadur RD, Grzybowski AT, Galat V, Moskowitz IP, Ruthenburg AJ. Chromatin-enriched lncRNAs can act as cell-type specific activators of proximal gene transcription. Nat Struct Mol Biol. 2017 Jul; 24(7):596-603. PMID: 28628087; PMCID: PMC5682930.
      Citations: 48     Fields:    Translation:HumansCells
    18. Hattori T, Lai D, Dementieva IS, Kurosawa K, Zheng Y, Akin LR, Swist-Rosowska KM, Grzybowski AT, Koide A, Krajewski K, Strahl BD, Kelleher NL, Ruthenburg AJ, Koide S, Montaño SP. Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation. Proc Natl Acad Sci U S A. 2016 Feb 23; 113(8):2092-7. PMID: 26862167; PMCID: PMC4776465.
      Citations: 22     Fields:    Translation:HumansCells
    19. Werner MS, Ruthenburg AJ. Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes. Cell Rep. 2015 Aug 18; 12(7):1089-98. PMID: 26257179; PMCID: PMC5697714.
      Citations: 90     Fields:    Translation:HumansCells
    20. Rothbart SB, Dickson BM, Raab JR, Grzybowski AT, Krajewski K, Guo AH, Shanle EK, Josefowicz SZ, Fuchs SM, Allis CD, Magnuson TR, Ruthenburg AJ, Strahl BD. An Interactive Database for the Assessment of Histone Antibody Specificity. Mol Cell. 2015 Aug 06; 59(3):502-11. PMID: 26212453; PMCID: PMC4530063.
      Citations: 73     Fields:    Translation:HumansCells
    21. Grzybowski AT, Chen Z, Ruthenburg AJ. Calibrating ChIP-Seq with Nucleosomal Internal Standards to Measure Histone Modification Density Genome Wide. Mol Cell. 2015 Jun 04; 58(5):886-99. PMID: 26004229; PMCID: PMC4458216.
      Citations: 36     Fields:    Translation:HumansAnimalsCells
    22. Chen Z, Grzybowski AT, Ruthenburg AJ. Traceless semisynthesis of a set of histone 3 species bearing specific lysine methylation marks. Chembiochem. 2014 Sep 22; 15(14):2071-5. PMID: 25155436; PMCID: PMC4415702.
      Citations: 8     Fields:    Translation:HumansCells
    23. Hattori T, Taft JM, Swist KM, Luo H, Witt H, Slattery M, Koide A, Ruthenburg AJ, Krajewski K, Strahl BD, White KP, Farnham PJ, Zhao Y, Koide S. Recombinant antibodies to histone post-translational modifications. Nat Methods. 2013 Oct; 10(10):992-5. PMID: 23955773; PMCID: PMC3828030.
      Citations: 31     Fields:    Translation:HumansAnimalsCells
    24. Mohrig JR, Beyer BG, Fleischhacker AS, Ruthenburg AJ, John SG, Snyder DA, Nyffeler PT, Noll RJ, Penner ND, Phillips LA, Hurley HL, Jacobs JS, Treitel C, James TL, Montgomery MP. Does activation of the anti proton, rather than concertedness, determine the stereochemistry of base-catalyzed 1,2-elimination reactions? Anti stereospecificity in E1cB eliminations of ß-3-trifluoromethylphenoxy esters, thioesters, and ketones. J Org Chem. 2012 Mar 16; 77(6):2819-28. PMID: 22321002.
      Citations:    Fields:    Translation:Cells
    25. Malecek K, Ruthenburg A. Validation of histone-binding partners by peptide pull-downs and isothermal titration calorimetry. Methods Enzymol. 2012; 512:187-220. PMID: 22910208.
      Citations: 4     Fields:    Translation:Cells
    26. Werner M, Ruthenburg AJ. The United States of histone ubiquitylation and methylation. Mol Cell. 2011 Jul 08; 43(1):5-7. PMID: 21726805.
      Citations: 8     Fields:    
    27. Ruthenburg AJ, Li H, Milne TA, Dewell S, McGinty RK, Yuen M, Ueberheide B, Dou Y, Muir TW, Patel DJ, Allis CD. Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions. Cell. 2011 May 27; 145(5):692-706. PMID: 21596426; PMCID: PMC3135172.
      Citations: 190     Fields:    Translation:HumansAnimalsCells
    28. Milne TA, Kim J, Wang GG, Stadler SC, Basrur V, Whitcomb SJ, Wang Z, Ruthenburg AJ, Elenitoba-Johnson KS, Roeder RG, Allis CD. Multiple interactions recruit MLL1 and MLL1 fusion proteins to the HOXA9 locus in leukemogenesis. Mol Cell. 2010 Jun 25; 38(6):853-63. PMID: 20541448; PMCID: PMC2902588.
      Citations: 121     Fields:    Translation:HumansAnimalsCells
    29. Ruthenburg AJ, Li H, Patel DJ, Allis CD. Multivalent engagement of chromatin modifications by linked binding modules. Nat Rev Mol Cell Biol. 2007 Dec; 8(12):983-94. PMID: 18037899; PMCID: PMC4690530.
      Citations: 540     Fields:    Translation:HumansAnimalsCells
    30. Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol. 2007 Nov; 14(11):1025-1040. PMID: 17984965; PMCID: PMC4691843.
      Citations: 698     Fields:    Translation:HumansCells
    31. Ruthenburg AJ, Allis CD, Wysocka J. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol Cell. 2007 Jan 12; 25(1):15-30. PMID: 17218268.
      Citations: 590     Fields:    Translation:HumansAnimalsCells
    32. Dou Y, Milne TA, Ruthenburg AJ, Lee S, Lee JW, Verdine GL, Allis CD, Roeder RG. Regulation of MLL1 H3K4 methyltransferase activity by its core components. Nat Struct Mol Biol. 2006 Aug; 13(8):713-9. PMID: 16878130.
      Citations: 425     Fields:    Translation:HumansCells
    33. Ruthenburg AJ, Wang W, Graybosch DM, Li H, Allis CD, Patel DJ, Verdine GL. Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex. Nat Struct Mol Biol. 2006 Aug; 13(8):704-12. PMID: 16829959; PMCID: PMC4698793.
      Citations: 119     Fields:    Translation:HumansCells
    34. Losey HC, Ruthenburg AJ, Verdine GL. Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA. Nat Struct Mol Biol. 2006 Feb; 13(2):153-9. PMID: 16415880.
      Citations: 97     Fields:    Translation:Cells
    35. Wei H, Ruthenburg AJ, Bechis SK, Verdine GL. Nucleotide-dependent domain movement in the ATPase domain of a human type IIA DNA topoisomerase. J Biol Chem. 2005 Nov 04; 280(44):37041-7. PMID: 16100112.
      Citations: 64     Fields:    Translation:HumansCells
    36. Ruthenburg AJ, Graybosch DM, Huetsch JC, Verdine GL. A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias. J Biol Chem. 2005 Jul 15; 280(28):26177-84. PMID: 15897198.
      Citations: 51     Fields:    Translation:Cells
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